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Sample GSM5968832 Query DataSets for GSM5968832
Status Public on Mar 23, 2023
Title YZ3_ESR1SUZ12E3Y
Sample type SRA
 
Source name Ishikawa
Organism Homo sapiens
Characteristics cell line: endometrial adenocarcinoma
fraction: ChIP
treatment: Treated with Estriol for 24 hours, first IP with ERS1 antibody, then for the second IP with SUZ12
Treatment protocol Ishikawa cells (~70% confluence) were transfection with 40ug of either pcDNA 3.1(+)/Flag-ERα or pcDNA /Flag-ERβ for 18 hours and subsequently treated with E3 for another 24 hours .
Growth protocol Ishikawa cells were maintained in MEM (Sigma-Aldrich, MO) both containing 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
Samples are sequenced using 100bp paired-end sequencing on an Illumina HiSeq 4000 according to Illumina protocols.Briefly, approximately 5-10ng of DNA is cleaned up using Ampure XP SPRI beads (Beckman Coulter Genomics). The DNA is then end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles). Indexed libraries that meet appropriate cut-offs are quantified by both RT-qPCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX. Samples with a yield of ≥0.5 ng/µl are used for sequencing. Flow Cell Preparation and Sequencing: Sample concentrations are normalized to 1 nM and loaded onto an Illumina HiSeq4000 flow cell at a concentration that yields 25 - 50 million passing filter clusters per sample. Samples are sequenced using 100bp paired-end sequencing on an Illumina HiSeq 4000 according to Illumina protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Data generated during sequencing runs are simultaneously transferred to the YCGA high-performance computing cluster
Supplementary files format and content: bedGraph
 
Submission date Mar 24, 2022
Last update date Mar 24, 2023
Contact name Yuping Zhou
E-mail(s) joezhouyp@gmail.com
Organization name Yale
Department OB/GYN
Lab Taylor Lab
Street address 310 cedar street
City new haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL16791
Series (2)
GSE199214 The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract
GSE199293 The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [ChIP-Seq]
Relations
BioSample SAMN26903077
SRA SRX14592980

Supplementary file Size Download File type/resource
GSM5968832_Sample_Yz-3.bedGraph.gz 35.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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